README.md

retrocookie.sh

You can add changes back to a template folder using the retrocookie python package. This fork fixes use of multiple template folders.

The retrocookie.sh --help documentation:

usage: retrocookie.sh [OPTION]... project_folder cc_config

Convert modified cookiecutter output back to it's template form.

Options:

-h, --help, help ... Show this help then exit.

-d .... Template subdirectory to use from multi-template repository url.
        Value=datajoint-workflow

-n .... Conda environment name that contains cookiecutter.
        Value=cookies

-i .... Ignore a file/folder from commits by adding it to .gitignore


Positional args:

project_folder .... The directory corresponding to the output of the original
                    cookiecutter command.
                    Value=my_project_dir
cc_config ......... Path to the 'cookiecutterc.yml' file with preconfigured values.
                    Value=my_project_dir/.cookiecutter.json

Temporary copy directory:

/var/folders/t3/wwync7qs1753cd1nzlqnzt900000gn/T/cookie_retro/datajoint-workflow

Examples:

 Regenerate to directory 'build' using previously specified values.
   > ./retrocookie.sh path/to/workflow_name

 Regenerate to current directory using a different repo and branch, also conda env.
   > ./retrocookie.sh -d datajoint-workflow -n cookies path/to/workflow_name

Requirements

• conda environment with required packages installed
  • tomli,
  • pyyaml
  • cookiecutter
  • retrocookie
• bash with rsync and git found in PATH.
• A project generated from a cookiecutter template.
• a .cookiecutter.json file with the user specified values filled in. This will be automatically generated at the root of the project folder.

Example Usage

1. Install cookiecutter as outlined here.

2. Install retrocookie: pip install 'git+https://github.com/iamamutt/retrocookie'

3. Clone the repo contents.

   • git clone https://github.com/datajoint-company/dj-cookiecutter.git
   • Optional: Edit dj-cookiecutter/tests/integration/fixtures/cookiecutterc.yml. The rest of the instructions below assume these default values.

4. Use the template.

   • cookiecutter -f --no-input --config-file=dj-cookiecutter/tests/integration/fixtures/cookiecutterc.yml --directory=datajoint-workflow -o /tmp dj-cookiecutter

5. Make some changes to files in /tmp/science-institute_brain-lab.

6. Run retrocookie.sh

   • dj-cookiecutter/datajoint-workflow/scripts/retrocookie/retrocookie.sh /tmp/science-institute_brain-lab

Note: If you run into merge conflicts, see the help for git-cherry-pick.